[1362] | 1 | Duchamp version 1.6 (2014/04/24) |
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| 2 | -------------------------------- |
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| 3 | |
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| 4 | Improvements and bug fixes: |
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| 5 | |
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| 6 | * When searching for negative features while using baseline |
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| 7 | subtraction, the parameterisation of the resulting detections was |
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| 8 | not being done correctly. Duchamp now correctly identifies the peak |
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| 9 | absorption location and measures the peak as being the peak |
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| 10 | absorption from the fitted continuum level. A future release will |
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| 11 | add more absorption-line-oriented parameters. |
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| 12 | |
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| 13 | * The way the borders of detections are displayed in annotation files |
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| 14 | has been improved. Duchamp now writes them in a polygon or |
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| 15 | join-the-dots fashion. This reduces the size of the annotation |
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| 16 | files, and is now compatible with the CASA viewer. |
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| 17 | |
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| 18 | * The VOTables now refer to version 1.3 of the VOTable schema. Note |
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| 19 | that they still use the old COOSYS method of specifying the |
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| 20 | coordinates. Moving to the preferred STC method will happen in a |
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| 21 | future release. |
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| 22 | |
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| 23 | * There were some problems with the storage and recovery of parameters |
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| 24 | in the binary catalogue - these have been fixed. |
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| 25 | |
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| 26 | * The BITPIX keyword in the mask FITS files that Duchamp writes are |
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| 27 | now SHORT_IMG, although they can be bigger if warranted by the |
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| 28 | number of objects. |
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| 29 | |
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| 30 | * Some UCDs in the VOTable were missing semicolons between elements. |
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| 31 | |
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| 32 | Documentation improvmements |
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| 33 | |
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| 34 | * The InputComplete file is more up-to-date, and has information on |
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| 35 | the type and default values of each possible input parameter (this |
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| 36 | information is also reflected in the User Guide). This is in |
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| 37 | preparation for a parameter editing GUI that will be released in a |
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| 38 | forthcoming version. |
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| 39 | |
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| 40 | * The User's Guide now has a section on common installation issues, |
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| 41 | based on feedback and experience with new users. |
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| 42 | |
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| 43 | Build changes: |
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| 44 | |
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| 45 | * Duchamp is now linked with the C++ compiler. Accordingly, the |
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| 46 | configure script searches for libgfortran when the gfortran compiler |
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| 47 | is specified (ie. has been used to build pgplot). |
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| 48 | |
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| 49 | * To allow Duchamp to build on Mac OS X 10.9 (Mavericks), configure |
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| 50 | searches for the libc++ library as well as stdc++. Duchamp has been |
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| 51 | successfully built on 10.9, with fresh installs of pgplot (5.2), |
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| 52 | wcslib (4.20) and cfitsio (3.36), but, as always, your mileage may |
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| 53 | vary. Please contact me via the Trac tickets if you encounter |
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| 54 | problems. |
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| 55 | |
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| 56 | * A number of warnings that came to light with the change to XCode |
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| 57 | XXXXX on the Mac have been fixed, and to gcc-4.4.5 on debian. |
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| 58 | |
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| 59 | |
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| 60 | Code base changes: |
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| 61 | |
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| 62 | * There are new wcs-pix conversion functions in fitsHeader that allow |
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| 63 | the specification of a single set of pixel and world coordinates |
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| 64 | (rather than arrays). |
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| 65 | |
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| 66 | * There is cleaner separation of the writing functions in the |
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| 67 | VOTableCatalogueWriter class. |
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| 68 | |
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| 69 | * The management of the wavelet filters has been improved, with new |
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| 70 | classes to handle the different filter types. The interface is |
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| 71 | largely the same, however. |
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| 72 | |
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| 73 | * There are improved front-end functions for the writing of arrays to |
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| 74 | the various FITS files. |
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| 75 | |
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[1286] | 76 | Duchamp version 1.5 (2013/08/29) |
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[1249] | 77 | -------------------------------- |
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| 78 | |
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[1280] | 79 | New features & algorithms: |
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[1249] | 80 | |
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| 81 | * There is now a more flexible way to specify channels that should be |
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| 82 | ignored by the source-finding. Use flaggedChannels to provide a list |
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| 83 | of single channels or channel ranges that should be ignored. This |
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| 84 | replaces the flagMW/minMW/maxMW parameters, extending their |
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| 85 | functionality and allowing more than one set of channels to be |
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| 86 | specified. |
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| 87 | |
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[1278] | 88 | * There is now an alternative way to find (and remove) spectral |
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| 89 | baselines, using a median baselining algorithm. This calculates the |
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| 90 | baseline value for a given pixel to be the median value within a box |
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| 91 | of a specified size centred on that pixel. There are two input |
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| 92 | parameters now available, baselineType (atrous or median), and |
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| 93 | baselineBoxWidth (the width of the median box). Consult the User's |
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| 94 | Guide for further information. |
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| 95 | |
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[1280] | 96 | * There is now more flexibility in running the spatial smoothing. The |
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| 97 | cutoff value in determining the size of the smoothing kernel can now |
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| 98 | be set via the input parameters, as can the way the edge pixels get |
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| 99 | treated. Conult the User's Guide for details. |
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| 100 | |
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[1287] | 101 | * You can now also specify the maximum number of voxels, spatial |
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| 102 | pixels and/or channels, in a way analogous to the minimum |
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| 103 | values. Detections with more than the maximum are rejected. Negative |
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| 104 | values (such as the defaults) mean this comparison is not done. |
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| 105 | |
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[1274] | 106 | Output changes: |
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| 107 | |
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| 108 | * The results files now include the Nchan and Nspatpix columns, |
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| 109 | showing the number of distinct channels and the number of spatial |
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| 110 | pixels in each detection. For clarity, the Npix column has been |
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| 111 | renamed Nvoxel. |
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| 112 | |
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| 113 | * The VOTable now includes the pixel location X, Y, Z columns, and the |
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| 114 | pixel ranges - this makes it much closer to the ASCII results file |
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| 115 | (it is just missing the string versions of RA/DEC, and F_tot when |
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| 116 | F_int is calculated). |
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| 117 | |
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[1266] | 118 | Bug fixes: |
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[1249] | 119 | |
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[1266] | 120 | * Negative velocity (and other) values were resulting in the column |
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| 121 | widths not adjusting correctly, leading to columns running into each |
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| 122 | other. This has been fixed, so that the spacing in the results files |
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| 123 | should be correct. |
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| 124 | |
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[1270] | 125 | * Fixed a problem applicable to cubes with blank/masked pixels in the |
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| 126 | same spectra as detections. The velocity width calculations could |
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| 127 | sometimes fail due to the mask not being applied. |
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[1266] | 128 | |
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[1249] | 129 | Code changes: |
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| 130 | |
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| 131 | * The plotting code has been refactored, improving its class structure |
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| 132 | and inheritance. No functional change from this should be evident, |
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| 133 | but it improves the maintainability of the code. |
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| 134 | |
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| 135 | |
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[1229] | 136 | Duchamp version 1.4 (2013/06/20) |
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| 137 | -------------------------------- |
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| 138 | |
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| 139 | Installation: |
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| 140 | |
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| 141 | * The "make lib" command will now create a shared library |
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| 142 | libduchamp.1.4.so as well as the static library libduchamp.1.4.a |
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| 143 | (formerly just called libduchamp.a). |
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| 144 | |
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| 145 | Bug Fixes: |
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| 146 | |
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| 147 | * The orientation of ellipses in the DS9 region files are now correct |
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| 148 | (they were wrong by 90 degrees). |
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| 149 | |
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| 150 | * Corrected the output FITS filenames so that they work when the input |
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| 151 | filename does *not* end in ".fits". |
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| 152 | |
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| 153 | Code changes: |
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| 154 | |
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| 155 | * The code that manages the output columns for the ASCII and VOTable |
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| 156 | output has been overhauled and streamlined. Little functional change |
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| 157 | should be evident, but it should be much more robust. And easier to |
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| 158 | use in derived software. |
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| 159 | |
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[1213] | 160 | Duchamp version 1.3.2 (2013/05/02) |
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| 161 | ---------------------------------- |
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| 162 | |
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| 163 | Bug fixes: |
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| 164 | |
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| 165 | * The units for the integrated flux (for F_int) were not being |
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| 166 | calculated for cases of a FITS file without a spectral |
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| 167 | axis. Additionally, a vestigial default value meant this column had |
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| 168 | units of "counts". This has been fixed so that a FITS file with |
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| 169 | Jy/beam units will have F_int values in Jy. |
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| 170 | |
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| 171 | * The ellipse fitting to find the MAJ/MIN/PA was not working correctly |
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| 172 | in the case of negative searches. This has been fixed. |
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| 173 | |
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| 174 | * The scaling of MAJ/MIN values was not being done correctly in all |
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| 175 | cases, so that the values were out by a factor of 60 or 3600. This |
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| 176 | was particularly the case when the ellipse fitting failed (due to |
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| 177 | small numbers of pixels, for instance). |
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| 178 | |
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| 179 | * The principle axes calculations have been simplified slightly, and |
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| 180 | now are done only on pixels above half the peak in the moment-0 map |
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| 181 | (to estimate the FWHM). |
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| 182 | |
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[1202] | 183 | Duchamp version 1.3.1 (2013/04/18) |
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| 184 | ---------------------------------- |
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| 185 | |
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| 186 | Bug fixes: |
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| 187 | |
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| 188 | * The kernel used in the 2D smoothing was not normalised properly, |
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| 189 | which meant the fluxes in the smoothed array were scaled |
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| 190 | incorrectly. The kernel is now normalised, so that the fluxes in the |
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| 191 | smoothed array decrease (and to an increasing degree with larger |
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| 192 | kernels, as expected). |
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| 193 | |
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| 194 | * The way the position angle of the smoothing kernel was interpreted |
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| 195 | was wrong. It now conforms to the typical astronomical position |
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| 196 | angle definition of degrees east of north. |
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| 197 | |
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| 198 | * The Z_PEAK column was being left out of the results file for |
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| 199 | Duchamp-1.3. It has been put back in. |
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| 200 | |
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| 201 | * The calculation of S/Nmax has changed so that when smoothing or |
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| 202 | reconstruction is done, the peak flux used is measured in the |
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| 203 | reconstructed/smoothed array (where the noise is measured). |
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| 204 | |
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| 205 | * The flux errors are now not reported in the case of smoothing, since |
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| 206 | we don't measure the noise in the original input image array. |
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| 207 | |
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| 208 | Other fixes: |
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| 209 | |
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| 210 | * The vertical range of the spectral plots now properly takes into |
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| 211 | account all spectra (not just the input array), and quirks with a MW |
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| 212 | range lying outside the plotted range have been fixed. |
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| 213 | |
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| 214 | * The flux scaling for the moment-0 map plot now ignores negative |
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| 215 | values, meaning the scale should be sensible. |
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| 216 | |
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| 217 | * The spelling of the Object2D::getPrincipalAxes() has been corrected. |
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| 218 | |
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| 219 | * Minor code optimisations have been made to the smoothing code. |
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| 220 | |
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| 221 | * The subsection class is now initialised with a blank string. |
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| 222 | |
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[1181] | 223 | Duchamp version 1.3 (2013/03/08) |
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| 224 | -------------------------------- |
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[1150] | 225 | |
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| 226 | New features: |
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| 227 | |
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[1159] | 228 | * New source parameters: |
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[1150] | 229 | |
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[1159] | 230 | # Each source now has a measurement of the major & minor axis sizes, |
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| 231 | along with the position angle of the major axis. The sizes are the |
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| 232 | full-width at half maximum, measured from the moment-0 map. These |
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| 233 | now appear in the catalogue and in the spectral plots, with the |
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| 234 | ellipse drawn on the moment map cutout in the spectral plots. The |
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| 235 | old measurements of w_RA & w_DEC are still made and included in |
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| 236 | the full catalogue, but are no longer reported in the smaller |
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| 237 | catalogue printed to screen (nor in the XML/VOTable output). |
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[1150] | 238 | |
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[1159] | 239 | # Each source also now has a measurement of the error on the |
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| 240 | integrated and total fluxes. This is calculated from summing in |
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[1178] | 241 | quadrature the statistical noise on each detected voxel. This is |
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| 242 | from a request by Sara Shakouri. |
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[1150] | 243 | |
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[1159] | 244 | * Output files - new types and changes to the way they are written: |
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[1150] | 245 | |
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[1159] | 246 | # Ability to create CASA region format files showing the location of |
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| 247 | the detected sources. This is analogous to the Karma annotation |
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| 248 | files or DS9 region files, for use with the casa viewer, but can |
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| 249 | also be imported into casapy. |
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[1150] | 250 | |
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[1159] | 251 | # Ability to save baseline values to a FITS file (in the same way as |
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| 252 | for the reconstructed or smoothed array). |
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[1150] | 253 | |
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[1159] | 254 | # Ability to save the moment-0 mask to a FITS file (that is, a mask |
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| 255 | indicating which spatial pixels form part of the moment-0 map). |
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[1150] | 256 | |
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[1159] | 257 | # There is an improved way to store the detected pixels for later |
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| 258 | re-use. While previously the detected pixels were written as scans |
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| 259 | to the logfile, and then read in when the usePrevious flag was |
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| 260 | set, we now write the scans and other metadata to a binary |
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| 261 | catalogue that can be read in again. Writing as a binary file |
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| 262 | leads to much better compression of the data, particularly when |
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| 263 | combined with the run-length encoding. It is anticipated future |
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| 264 | tools will be provided to allow additional interaction with these |
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| 265 | binary catalogues. |
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| 266 | |
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| 267 | # There are slight changes to the format of the ASCII catalogues, |
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| 268 | where lines not containing sources are prefixed with a comment |
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| 269 | character '#'. This will facilitate their use in other software. |
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| 270 | |
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[1161] | 271 | * There is a new command-line parameter, -t THRESH, which specifies |
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| 272 | the flux threshold for searching. It is designed to be used with the |
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| 273 | -f option, as a quick way of searching a FITS image to a specified |
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| 274 | flux level. |
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[1159] | 275 | |
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[1150] | 276 | Bug fixes: |
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| 277 | |
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| 278 | * A bug in the spatial smoothing has been fixed. The mask was being |
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| 279 | interpreted incorrectly, so that no valid pixels were getting |
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| 280 | smoothed. |
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| 281 | |
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| 282 | * The WCS for the moment-0 FITS cube has been fixed (specifically, the |
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| 283 | axis names). |
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| 284 | |
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| 285 | * When usePrevious was used, the behaviour in previous versions was to |
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| 286 | always write individual spectra. This is now controlled by a new |
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| 287 | parameter flagPlotIndividualSpectra. |
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| 288 | |
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| 289 | * Minor improvements to the output when verbose=false. |
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| 290 | |
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| 291 | * Improvements to the Makefile, so that header files from a |
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| 292 | previously-installed version of Duchamp do not get used instead of |
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| 293 | those from the current version. |
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| 294 | |
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| 295 | * The vertical range for the spectral plots now take into account the |
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| 296 | baseline and reconstructed/smoothed arrays as well (outside of any |
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| 297 | MW range, of course). |
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| 298 | |
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| 299 | Other |
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| 300 | |
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| 301 | * The code-base for reading from and writing to FITS files has been |
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| 302 | overhauled and streamlined. It can now be found in the FitsIO |
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[1180] | 303 | directory. The interface for the writing of FITS files via the Cube |
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| 304 | class has not changed. |
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[1150] | 305 | |
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[1161] | 306 | * The User Guide has been slightly re-ordered to provide more explicit |
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| 307 | information about the source parameters. |
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[1150] | 308 | |
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[1161] | 309 | |
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[1107] | 310 | Duchamp version 1.2.2 (2012/10/29) |
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| 311 | ---------------------------------- |
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| 312 | |
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| 313 | Bug fixes: |
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| 314 | |
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| 315 | * The reading of reconstructed & smoothed arrays in the case of large |
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| 316 | (>2GB) cubes has been improved. While the most recent versions of |
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| 317 | cfitsio were able to handle these, earlier versions would result in |
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| 318 | a segementation fault using the previous interface. An alternative |
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| 319 | interface has been implemented that avoids these faults, even for |
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| 320 | the older cfitsio libraries. |
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| 321 | |
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| 322 | * A bug affecting the writing of FITS mask files (apparently for the |
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| 323 | case of flagging by the object number) has been fixed. |
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| 324 | |
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| 325 | * The moment map occasionally failed if sources lay spatially within |
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| 326 | the blank pixel region of the first channel. This check has been |
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| 327 | removed and the moment map should be produced successfully in all |
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| 328 | situations. |
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| 329 | |
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| 330 | Other: |
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| 331 | |
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| 332 | * The UCDs used in the VOTable catalogue output have been |
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| 333 | updated. Several of these were shared between different columns, and |
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| 334 | so they have been changed so that each UCD is unique to one |
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| 335 | column. The column ID strings have been updated for clarity. |
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| 336 | |
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| 337 | * The determination of default output image filenames has been |
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| 338 | improved -- it previously assumed the input filename ended in |
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| 339 | '.fits', but this is no longer the case. |
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| 340 | |
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[1087] | 341 | Duchamp version 1.2.1 (2012/10/09) |
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| 342 | ---------------------------------- |
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| 343 | |
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| 344 | New feature: |
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| 345 | |
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| 346 | * Duchamp can now produce region files to annotate images displayed in |
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| 347 | SAOImage DS9. There are new parameters flagDS9 and ds9File that work |
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| 348 | in the same way as the Karma annotation file parameters. The region |
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| 349 | files can also be displayed in (at least some versions of) |
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| 350 | casaviewer. |
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| 351 | |
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| 352 | * There is a new script to fix occasional problems with the |
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| 353 | automatically-detected Makefile, and the verification script has |
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| 354 | been updated and improved. |
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| 355 | |
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| 356 | Bug fixes: |
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| 357 | |
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| 358 | * The main bug fix for this release corrects a problem with the |
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| 359 | velocity width measurements made when searching for negative |
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| 360 | detections. It was possible to get very small (and incorrect) widths |
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| 361 | in some cases - this was due to the integrated spectrum not being |
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| 362 | inverted correctly. |
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| 363 | |
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| 364 | * In the case of smoothing, the stats of the full cube that were being |
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| 365 | reported in the output files were actually those of the un-smoothed |
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| 366 | (input cube). This only affected the output files, not the detection |
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| 367 | process itself. |
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| 368 | |
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| 369 | * The units were not being reported in the VOTable. This has been |
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| 370 | fixed. |
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| 371 | |
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| 372 | * The UCDs for the spectral parameters in the VOTable were not being |
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| 373 | adapted to the user requests, so didn't always match the types of |
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| 374 | the parameters. All should be consistent now. |
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| 375 | |
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| 376 | Other changes: |
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| 377 | |
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| 378 | * The codebase relating to the creation of and writing to output files |
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| 379 | (results, logs, annotation, VOTables) has been overhauled, with a |
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[1088] | 380 | cleaner interface. Most of this code is in the new subdirectory |
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| 381 | src/Outputs, to where the columns code has been moved as well. |
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[1087] | 382 | |
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[1088] | 383 | This was instigated by ASKAP/Selavy development, but also allowed |
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| 384 | the expansion of output formats to include DS9 region files. No |
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| 385 | change to the user should be visible, but anyone using the software |
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| 386 | will notice differences. Please get in touch if changes are |
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| 387 | difficult to follow. |
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| 388 | |
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[1035] | 389 | Duchamp version 1.2 (2012/08/08) |
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[962] | 390 | -------------------------------- |
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[928] | 391 | |
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[951] | 392 | Key changes: |
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| 393 | |
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| 394 | * The way the wavelet reconstruction is done in the presence of BLANK |
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| 395 | voxels is slightly different, specifically when there were BLANK |
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| 396 | voxels on the edge. While BLANK voxels are always ignored by the |
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| 397 | reconstruction (and left in place), the previous approach dealt with |
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| 398 | BLANKS on the edge by moving the effective edge of the image inwards |
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| 399 | until the first non-blank voxel. This meant that the size of the |
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| 400 | dimensions used to determine the number of scales, and the location |
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| 401 | where boundary reflections took place where different to the input |
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| 402 | image size. |
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| 403 | |
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| 404 | However, this meant that BLANK voxels on the edge were treated |
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| 405 | differently to those not on the edge, so this inconsistency was |
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| 406 | removed. The full image dimensions are always used to calculate the |
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| 407 | number of scales, and reflections (which is how the reconstruction |
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| 408 | deals with the boundaries) will occur at the actual image edges. |
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| 409 | |
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| 410 | If your data has this property (BLANK pixels at the image |
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| 411 | boundaries), then any reconstruction will be affected (most likely |
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| 412 | only in a small way) and potentially any subsequent searching. You |
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[1035] | 413 | are advised to check this (for instance by saving the results of the |
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| 414 | resonstruction from 1.1.13 and 1.2 and comparing). |
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[951] | 415 | |
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[1035] | 416 | * The way the spectral world coordinate system is dealt with has been |
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| 417 | improved. Previously Duchamp tried to convert to a velocity axis, |
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| 418 | and got a bit grumpy if that didn't work well. Now it will express |
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| 419 | the spectral units in the axis type indicated by the FITS |
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| 420 | header. Duchamp will also allow you to change this type by providing |
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| 421 | an appropriate WCS type as an input parameter. You may also provide |
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| 422 | a rest frequency in the parameter file and this will be used to |
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| 423 | calculate velocities. And, as before, you can provide specific units |
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| 424 | for the spectral quantities to be converted into. |
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| 425 | |
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[951] | 426 | * Since v1.1.13 was released, the journal paper describing Duchamp has |
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| 427 | been published. It can be found at MNRAS 421, 3242 (2012), or |
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| 428 | http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2012.20548.x/full. It |
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| 429 | includes descriptions of the various algorithms used for Duchamp, as |
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| 430 | well as some indicative comparisons of the relative completeness & |
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| 431 | reliability. Please cite this paper when describing Duchamp. |
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| 432 | |
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| 433 | Other new features: |
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| 434 | |
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[1035] | 435 | * The default value of snrCut has changed from 3 to 5. This is |
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| 436 | espeically important if you use the -f option, but also if you don't |
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| 437 | provide snrCut in your parameter file. |
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| 438 | |
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[951] | 439 | * The XML VOTable output now includes a more complete list of |
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| 440 | parameters, matching the output given in text form in the results & |
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| 441 | log output files. Only those parameters affecting the results are |
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| 442 | included - things like the output file names and so on are left out. |
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| 443 | |
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| 444 | * The minVoxels parameter is now adjusted to be at least (minPix + |
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| 445 | minChannels - 1). If it is changed, a warning message is triggered. |
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| 446 | |
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| 447 | * The warning/error reporting has been overhauled, with an improved |
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| 448 | interface for developers. Also, some ERROR instances that previously |
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| 449 | resulted in the program terminating now allow it to continue |
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| 450 | (provided that is possible given the error). |
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| 451 | |
---|
[1026] | 452 | * It is now possible to give the convergence criterion for the wavelet |
---|
| 453 | reconstruction via the parameter reconConvergence. When the relative |
---|
| 454 | change in standard deviation of the residuals from the |
---|
| 455 | reconstruction falls below this value, the a trous algorithm stops |
---|
| 456 | iterating. |
---|
| 457 | |
---|
[991] | 458 | * The way one-dimensional arrays were dealt with was unsatisfactory, |
---|
| 459 | both with the way positions were registered and the format of the |
---|
| 460 | graphical output. Improvements have been made such that a 1D data |
---|
| 461 | structure is assumed to be a spectrum, and so positions in the |
---|
| 462 | spectrum are reported as z-pixels (or the equivalent world |
---|
| 463 | coordinate). Instead of a 2D moment map, the X-windows display will |
---|
| 464 | show the spectrum with all detected pixels plus the final list of |
---|
| 465 | detections highlighted, along with the detection and growth |
---|
[1035] | 466 | thresholds. This plot will also be written to the "detectionMap" |
---|
| 467 | image. |
---|
[991] | 468 | |
---|
| 469 | * All spectral plots will now show the detection (and growth, if |
---|
| 470 | applicable) thresholds when plotting the peak flux spectrum. |
---|
| 471 | |
---|
| 472 | * Accessing FITS files when a subsection string is provided has been |
---|
| 473 | streamlined. The cfitsio package, which handles the FITS access, |
---|
| 474 | creates a temporary file containing this image section, and this |
---|
| 475 | meant the previous approach was slow, particularly for large |
---|
| 476 | files/sections. Now the file is only opened once and the overhead of |
---|
| 477 | creating the temporary file is only encountered once. |
---|
| 478 | |
---|
| 479 | * Several aspects of the processing & output did not handle a |
---|
| 480 | non-existent WCS well. This has been improved, so that all stages of |
---|
| 481 | execution will proceed without errors. |
---|
| 482 | |
---|
[928] | 483 | Bug fixes: |
---|
| 484 | |
---|
[941] | 485 | * The absence of a BLANK keyword when trimming will now not trigger a |
---|
| 486 | failure, only a warning message. |
---|
[928] | 487 | |
---|
[941] | 488 | * The flux unit conversion (eg. from Jy/beam to mJy/beam) was not |
---|
| 489 | being applied correctly when an existing reconstructed or smoothed |
---|
| 490 | array was being read in. This is now applied properly. |
---|
| 491 | |
---|
| 492 | * When saving reconstructed or smoothed arrays, the data type is now |
---|
| 493 | set to FLOAT, so that the correct values are written (and |
---|
| 494 | subsequently read in). The previous version was potentially saving |
---|
| 495 | to a FITS file with integer data type (this depended on the type of |
---|
[951] | 496 | the input array). In this case, the full precision of data values |
---|
| 497 | would not be preserved, so reading back in and doing an identical |
---|
| 498 | search could yield different sources. |
---|
[941] | 499 | |
---|
| 500 | * For certain cases, the reconstruction attempted to use a very large |
---|
| 501 | number of scales. This has been fixed. |
---|
| 502 | |
---|
[1026] | 503 | * The maximum scale for the reconstruction was not always being |
---|
| 504 | applied. The scale ranges are now enforced for all types of |
---|
| 505 | reconstructions. |
---|
| 506 | |
---|
[941] | 507 | * When saving a mask image while using a subsection of a cube, the |
---|
| 508 | offsets for the subsection were not being accounted for |
---|
| 509 | correctly. This is now fixed. |
---|
| 510 | |
---|
[991] | 511 | * The detection map plots were not recording pixels added from the |
---|
| 512 | growing stage. This has been fixed. |
---|
| 513 | |
---|
[941] | 514 | * The RA & Dec now have appropriate precision, rather than an |
---|
| 515 | arbitrary 2 decimal places on the seconds value. The RA will be one |
---|
| 516 | decimal place more than the Dec, and they will reflect the degree of |
---|
| 517 | precision in the image pixels. |
---|
| 518 | |
---|
| 519 | * A number of data type conversions (typically ints to floats) led to |
---|
| 520 | errors in some calculations, such as WCS conversions. Care has been |
---|
| 521 | taken to make sure all indexing is done appropriately with no |
---|
| 522 | overflow, and that all conversions (where necessary) are done |
---|
| 523 | appropriately. |
---|
| 524 | |
---|
| 525 | * It was possible to get world positions looking like 11:59:60.0! Not |
---|
| 526 | any more. |
---|
| 527 | |
---|
[1020] | 528 | * Reading previous detections from the log file (via the use of the |
---|
| 529 | usePrevious parameter) did result in error messages due to slightly |
---|
| 530 | incompatible formats. These have been fixed, and all graphical |
---|
| 531 | output should work properly. |
---|
[928] | 532 | |
---|
[1020] | 533 | * When using a spectral search, having a blank pixel in the first |
---|
| 534 | channel could lead to that entire spectrum being ignored, leading to |
---|
| 535 | inconsistent results between spectral and spatial searches. This |
---|
| 536 | issue has been fixed, with both types of searches returning the same |
---|
| 537 | catalogue. |
---|
| 538 | |
---|
| 539 | |
---|
[928] | 540 | Code base development notes: |
---|
| 541 | |
---|
[951] | 542 | * Most instances of integer overflow due to insufficient precision |
---|
| 543 | have been tracked down - many of these were indexing variables of |
---|
| 544 | type int, which have been changed to size_t. |
---|
[928] | 545 | |
---|
[1020] | 546 | * Importantly, for code interfacing with the duchamp::Cube and related |
---|
| 547 | classes, axisDim is now an array of size_t elements, rather than |
---|
| 548 | long. |
---|
| 549 | |
---|
[951] | 550 | * Object3D now carries its spatial map with it, rather than |
---|
| 551 | calculating it on the fly when requested. This saves a lot of |
---|
| 552 | unnecessary computational effort. |
---|
[928] | 553 | |
---|
[951] | 554 | * The warning/error interface has improved, making use of C++ |
---|
| 555 | exception handling. This should be compatible with external logging |
---|
| 556 | infrastructure (such as log4cxx). |
---|
| 557 | |
---|
[1035] | 558 | * The interface to the FitsHeader & WCS structures for external code |
---|
| 559 | has been improved, so that the WCS can be set up via function calls. |
---|
[951] | 560 | |
---|
| 561 | |
---|
| 562 | |
---|
[852] | 563 | Duchamp version 1.1.13 (2011/04/10) |
---|
| 564 | ------------------------------------- |
---|
| 565 | |
---|
| 566 | Bug fixes: |
---|
| 567 | |
---|
| 568 | * The median statistics calculations had a bug in the test for whether |
---|
| 569 | the array under consideration was of even size. The correction for |
---|
| 570 | this can mean small differences in the resulting values. This can |
---|
| 571 | flow through to calculated detection thresholds - please check this |
---|
| 572 | with your data if you use this mode! |
---|
| 573 | |
---|
| 574 | * The reconstruction code had a bug where the incorrect number of |
---|
| 575 | scales was being used. This occurred when the blank pixel flag was |
---|
| 576 | set, and when the spectral dimension was smaller than both the |
---|
| 577 | spatial dimensions. |
---|
| 578 | |
---|
| 579 | Other: |
---|
| 580 | |
---|
| 581 | * The default value of the blank pixel flag has been set to false, |
---|
| 582 | rather than true. For Duchamp, this should not matter, as it is set |
---|
| 583 | when the FITS file is read in. For external code using, for |
---|
| 584 | instance, the reconstruction algorithms, this default may be |
---|
| 585 | important. Having it true was contributing to the second bug listed |
---|
| 586 | above. It also makes more sense for it to be false unless explicitly |
---|
| 587 | set in some way. |
---|
| 588 | |
---|
| 589 | * The reconstruction code has been streamlined a little, reducing its |
---|
| 590 | memory impact and using more appropriate variable types |
---|
| 591 | (eg. unsigned ints instead of ints and so forth). |
---|
| 592 | |
---|
| 593 | * For those who care about the actual code base, the statistics |
---|
| 594 | functions have been expanded, and separated from getStats.cc into |
---|
| 595 | "normal" and "robust" versions. |
---|
| 596 | |
---|
| 597 | |
---|
[836] | 598 | Duchamp version 1.1.12 (2011/03/18) |
---|
| 599 | ------------------------------------- |
---|
| 600 | |
---|
| 601 | Bug fixes: |
---|
| 602 | |
---|
| 603 | * The velocity width calculations had a bug that occasionally led to |
---|
| 604 | very large values. The widths are calculated using the integrated |
---|
| 605 | spectrum, using a threshold relative to its peak. In v.1.1.10 and |
---|
| 606 | 1.1.11, however, the peak was searched for over the entire spectral |
---|
| 607 | range, rather than just the range for the current object. This led |
---|
| 608 | to spurious values. This has been fixed, so that the peak is only |
---|
| 609 | searched for within the detected ranage of the object. |
---|
| 610 | |
---|
| 611 | * Both the pixel and statistics subsections are now more carefully |
---|
| 612 | examined, with errors reported if there are no valid pixels in the |
---|
| 613 | pixel subsection, or if the statistics subsection does not intersect |
---|
| 614 | with the pixel subsection. |
---|
| 615 | |
---|
| 616 | Other: |
---|
| 617 | |
---|
| 618 | * The configure script has been slightly improved so that the pgsbox |
---|
| 619 | library is only added if PGPlot has been enabled - this is |
---|
| 620 | particularly necessary with the slightly changed build procedure for |
---|
| 621 | recent wcslib versions. |
---|
| 622 | |
---|
| 623 | * In a related note, one file - momentMap.cc - had some #include |
---|
| 624 | statements that failed when PGPlot (and hence pgsbox in WCSLIB) was |
---|
| 625 | not enabled. These were actually unnecesssary and have been removed. |
---|
| 626 | |
---|
| 627 | * There is a new input parameter - flagPlotSpectra - that allows the |
---|
| 628 | user to turn off the production of the spectral plots. It defaults |
---|
| 629 | to true (meaning the plots are produced). |
---|
| 630 | |
---|
| 631 | |
---|
[819] | 632 | Duchamp version 1.1.11 (2011/03/01) |
---|
[799] | 633 | ------------------------------------- |
---|
| 634 | |
---|
| 635 | Improvements: |
---|
| 636 | |
---|
| 637 | * The largest changes in this release involved improving the |
---|
| 638 | efficiency of the code, resulting in further speed-ups. The code |
---|
| 639 | affected was the low-level object-handling code, with the merging |
---|
| 640 | stages in particular showing good speed-ups. |
---|
| 641 | |
---|
| 642 | * The default value for the beam size, when the beam parameters are |
---|
| 643 | not in the FITS header, has been dropped. Now the default behaviour |
---|
| 644 | is to simply not make any beam corrections if the beam is not |
---|
| 645 | specified by either the FITS file or the input parameters. Thanks to |
---|
| 646 | Tobias Westemeier for the suggestion. |
---|
| 647 | |
---|
| 648 | * The reporting of the beam size has changed slightly to provide a bit |
---|
| 649 | more information. |
---|
| 650 | |
---|
| 651 | Bug Fixes: |
---|
| 652 | |
---|
[819] | 653 | * The statistics section (statSec) could be larger than the image |
---|
| 654 | subsection (if provided), yet the pixels required would never be |
---|
| 655 | read in from the FITS file. The behaviour has been changed so that |
---|
| 656 | the statSec, if requested, is trimmed to be wholly within the image |
---|
| 657 | section. |
---|
| 658 | |
---|
| 659 | * It was possible to request, for instance, spectral smoothing on a 2D |
---|
| 660 | image. This resulted in a blank smoothed array, which led to |
---|
| 661 | problems in the calculations of statistics (and hence the |
---|
| 662 | threshold), as well as subsequent calculations. This has been fixed, |
---|
| 663 | so that in cases like this the smoothing is turned off (and a |
---|
| 664 | warning message is displayed). |
---|
| 665 | |
---|
[799] | 666 | * There was a problem with using a MW range and subsectioning when |
---|
| 667 | growing objects, as a result of changes in 1.1.10. This has been |
---|
| 668 | fixed. |
---|
| 669 | |
---|
| 670 | * Inversion was failing when no array was allocated (not a problem for |
---|
| 671 | standard Duchamp, but affected its use as a library by other code). |
---|
| 672 | |
---|
[812] | 673 | * Writing text spectra would only occur when PGPlot output was enabled |
---|
| 674 | in the build (it was combined with the plotting of the spectral |
---|
[810] | 675 | graphs). This has been changed so that this output can be requested |
---|
[812] | 676 | without requiring PGPlot. |
---|
[810] | 677 | |
---|
[804] | 678 | * The equation for the beam size in Sec.4.2 of the User Guide was |
---|
| 679 | incorrect and has been fixed. |
---|
| 680 | |
---|
[819] | 681 | * Minor change to the configure script to improve the detection of the |
---|
| 682 | PGPlot library. |
---|
| 683 | |
---|
| 684 | Code development notes: |
---|
| 685 | |
---|
| 686 | * The main work has been additions and improvements to the interfaces |
---|
| 687 | for the Param and the Section classes, as well as new classes to |
---|
| 688 | manage the beam information. The efficiency changes mentioned above |
---|
| 689 | also affected the internals of some of the PixelInfo classes, and |
---|
| 690 | provided additional functions for judging the closeness of |
---|
| 691 | neighbouring objects. |
---|
| 692 | |
---|
[760] | 693 | Duchamp version 1.1.10 (2010/11/15) |
---|
[574] | 694 | ------------------------------------- |
---|
[542] | 695 | |
---|
[760] | 696 | Improvements: |
---|
| 697 | |
---|
| 698 | * The major change for this release is a greatly improved growing |
---|
| 699 | algorithm. The previous incarnation was very inefficient (testing |
---|
| 700 | all pixels in an object, most of which only have neighbours that are |
---|
| 701 | already in the object), and could take an unnecessarily large amount |
---|
| 702 | of time in the case of extended sources. The improved algorithm |
---|
| 703 | makes use of voxel flags to quickly identify those voxels not yet in |
---|
| 704 | an object and only examines them. For a certain test case |
---|
| 705 | (observations of extended Galactic HI), the time required reduced |
---|
[761] | 706 | from about a day to about a minute! (Note that compact sources, such |
---|
| 707 | as HI galaxies, will not show this degree of speedup...) Many thanks |
---|
| 708 | to Tara Murphy for pointing out this bug and her help in |
---|
| 709 | diagnosing/fixing the problem. |
---|
[760] | 710 | |
---|
| 711 | * There have been a number of further improvements to the code to |
---|
| 712 | speed it up, based on some profiling. The most important was the |
---|
| 713 | function to add pixels to a 2D object, but there were several other |
---|
| 714 | minor changes as well. |
---|
| 715 | |
---|
| 716 | * The minimum size of the detections can now also be specified in |
---|
| 717 | terms of the total number of voxels (in addition or instead of |
---|
| 718 | specifying the minimum spatial pixels or channels). |
---|
| 719 | |
---|
| 720 | * The way memory is allocated when reading the image has been |
---|
| 721 | streamlined. The amount of memory being allocated is also now |
---|
| 722 | reported - this is in an effort to allow users to identify problems |
---|
| 723 | with running out of memory. |
---|
| 724 | |
---|
| 725 | * The version number is now reported in the results and log files. |
---|
| 726 | |
---|
| 727 | * Only the filename of the input image (ie. not the leading |
---|
| 728 | directories) is now shown on the detection and moment-0 maps. This |
---|
| 729 | is to avoid problems with large directory paths being too wide for |
---|
| 730 | the plot. |
---|
| 731 | |
---|
| 732 | * The verification script was improved for readability (although no |
---|
| 733 | functional change was made). |
---|
| 734 | |
---|
| 735 | Bug fixes: |
---|
| 736 | |
---|
| 737 | * Growing was not being done when a single source was found. Now |
---|
| 738 | fixed. |
---|
| 739 | |
---|
| 740 | * For particular WCS setups, the RA can be interpreted as being |
---|
| 741 | negative, which corrupted the Source ID (ie. the IAU-format |
---|
| 742 | string). This has been fixed. |
---|
| 743 | |
---|
| 744 | * When the flux units were changed, problems had been seen when |
---|
| 745 | writing a reconstructed cube to a FITS file. Any unit change is now |
---|
| 746 | undone prior to writing and there should now be no problem. |
---|
| 747 | |
---|
| 748 | * Filenames with spaces in them were not handled well. New functions |
---|
| 749 | were included and moved to a more obvious location. These filenames |
---|
| 750 | now work as expected. |
---|
| 751 | |
---|
| 752 | * Spectral axes of type FREQ that had a rest frequency were not being |
---|
| 753 | put into velocity units. Now fixed. |
---|
| 754 | |
---|
| 755 | * Improvements to the output to screen, making sure everything is |
---|
| 756 | covered by the verbose flag. |
---|
| 757 | |
---|
| 758 | * Better management of the allocation of arrays. |
---|
| 759 | |
---|
| 760 | * The minSize parameter in Image was never initialised, leading to |
---|
| 761 | unpredictable behaviour. Now fixed. |
---|
| 762 | |
---|
| 763 | Code development notes: |
---|
| 764 | |
---|
| 765 | * New functionality includes: a function to return a vector list of |
---|
| 766 | voxels in an Object3D or Detection; a new generic Search function |
---|
| 767 | (basically a front-end to each of the individual functions); more |
---|
[766] | 768 | complete copy constructors for the DataArray classes; new methods |
---|
| 769 | for finding the velocity widths. |
---|
[760] | 770 | |
---|
| 771 | Duchamp version 1.1.9 (2010/03/26) |
---|
| 772 | ------------------------------------- |
---|
| 773 | |
---|
[654] | 774 | Improvements: |
---|
[616] | 775 | |
---|
[680] | 776 | * There is now the ability to save the moment-0 map as a FITS |
---|
| 777 | file. This is controlled by the parameters flagOutputMomentMap and |
---|
| 778 | fileOutputMomentMap, which work in the same way for the mask file. |
---|
| 779 | |
---|
[697] | 780 | * There is a new parameter flagRejectBeforeMerge that, when true, |
---|
[680] | 781 | rejects sources according to the minPix/minChannels requirements |
---|
| 782 | before the merging and growing is done. This defaults to false (so |
---|
| 783 | default behaviour is as before). Thanks to Tobias Westmeier for |
---|
| 784 | suggesting this and the above improvement. |
---|
| 785 | |
---|
[697] | 786 | * There is also a new parameter flagTwoStageMerging. When true (the |
---|
| 787 | default), newly-detected objects are merged with the first close |
---|
| 788 | object in the list. When false, they are simply added to the end of |
---|
| 789 | the list. In both cases, a second round of merging is done to pick |
---|
| 790 | up all close matches. |
---|
| 791 | |
---|
[680] | 792 | * The way the beam is specified in the absence of the BMAJ/BMIN/BPA |
---|
| 793 | parameters has been slightly changed. The use of "beamSize" was |
---|
| 794 | somewhat ambiguous (it meant the number of pixels covered by the |
---|
| 795 | beam, not the FWHM), so new parameters have been introduced. The |
---|
| 796 | beam can be specified by beamArea (which replaces beamSize), or |
---|
| 797 | beamFWHM (the FWHM of the beam in pixels). If beamFWHM is provided, |
---|
| 798 | it will be used, else the beamArea will be. |
---|
| 799 | |
---|
[687] | 800 | * There is a new parameter searchType that allows the user to choose |
---|
| 801 | how the searching is done. The behaviour up till now has been to |
---|
| 802 | search the 2D channel maps one at a time to build up the 3D |
---|
| 803 | detections. This is the default, and can be obtained by setting |
---|
| 804 | searchType=spatial. Alternatively, you can set searchType=spectral |
---|
| 805 | to do the searching in the 1D spectra. |
---|
| 806 | |
---|
[654] | 807 | * Profiling of the code has led to a few changes that have sped up |
---|
| 808 | some calculations, particularly those involving the median. Rather |
---|
| 809 | than using std::sort, the code now simply uses std::nth_element, |
---|
| 810 | which shows a substantial speedup factor. |
---|
| 811 | |
---|
| 812 | * When using the objectList parameter, the maps will now only show the |
---|
| 813 | selected objects, rather than all detected objects. |
---|
| 814 | |
---|
| 815 | * There is a new verification test that looks at the "growing" |
---|
| 816 | functionality. |
---|
| 817 | |
---|
| 818 | Bug fixes: |
---|
| 819 | |
---|
[670] | 820 | * When saving a mask FITS file, there was an occasional memory leak |
---|
| 821 | that caused Duchamp to crash (only when the cube was suitably |
---|
| 822 | large). This has been fixed. |
---|
| 823 | |
---|
[680] | 824 | * The median calculation had a bug that led to an incorrect value |
---|
| 825 | being reported. The difference will not be great (the element of an |
---|
| 826 | array being reported as the median was out by one), but could be |
---|
| 827 | noticeable depending on the dataset. |
---|
| 828 | |
---|
| 829 | * The MW range parameters did not respond to the use of a |
---|
| 830 | subsection. They should refer to channel ranges in the original |
---|
| 831 | cube, and changes have been made to the code to reflect this. |
---|
| 832 | |
---|
[654] | 833 | * There was an occasional error in writing out FITS keywords, due to |
---|
| 834 | the way comment strings were intialised. This has been improved and |
---|
| 835 | made more robust. |
---|
| 836 | |
---|
| 837 | * Testing with gcc-4.3.2 showed a number of compilation warnings & |
---|
| 838 | errors, which have been fixed. |
---|
| 839 | |
---|
| 840 | * The Gaussian smoothing kernel was too small - it is now made big |
---|
| 841 | enough to encompass all possible values. It was also being |
---|
| 842 | incorrectly scaled. This had no functional effect on the detection |
---|
| 843 | of objects, but for other uses was incorrect. This has been |
---|
| 844 | rectified. |
---|
| 845 | |
---|
| 846 | * Some outputs that weren't caught by the verbose flag now are. |
---|
| 847 | |
---|
| 848 | |
---|
| 849 | Code development notes: |
---|
| 850 | |
---|
| 851 | The following notes only apply if you want to use the code as a |
---|
| 852 | library, rather than the stand-alone package. These have generally |
---|
| 853 | come out of the ASKAP software development. If you just use the |
---|
| 854 | stand-alone package, they won't be a concern. |
---|
| 855 | |
---|
[616] | 856 | * The API for storing detected objects has changed, making it more |
---|
[654] | 857 | robust from a programming point of view. |
---|
[616] | 858 | |
---|
[654] | 859 | * Additional versions of some functions (and the Gaussian smoothing |
---|
| 860 | class) have been added - this has come out of the ASKAP development |
---|
| 861 | work. |
---|
| 862 | |
---|
| 863 | * A number of instances of "unsigned int" being used for loops have |
---|
| 864 | been changed to iterators or "size_t". There shouldn't be any |
---|
| 865 | functional change from this -- the code should just build more |
---|
| 866 | cleanly. |
---|
| 867 | |
---|
[687] | 868 | * The Detection class now records whether the parameters have been |
---|
| 869 | set, and unsets that flag when objects are merged. This allows |
---|
| 870 | external programs to track which objects have been merged and deal |
---|
| 871 | with them appropriately. |
---|
[654] | 872 | |
---|
[687] | 873 | |
---|
[616] | 874 | Duchamp version 1.1.8 (2009/07/20) |
---|
| 875 | ---------------------------------- |
---|
| 876 | |
---|
[542] | 877 | Improvements: |
---|
| 878 | |
---|
[572] | 879 | * The final source list can now be sorted on one of a range of object |
---|
| 880 | parameters: x-value, y-value, z-value, ra, dec, vel, w50, iflux, |
---|
| 881 | pflux (integrated and peak flux respectively), or snr. Simply use |
---|
| 882 | the new input parameter sortingParam. Its default value is vel, so |
---|
| 883 | the default behaviour stays the same. |
---|
| 884 | |
---|
[543] | 885 | * The FDR method involves calculating how many pixels are |
---|
| 886 | correlated. This previously involved multiplying the beam area by 2, |
---|
| 887 | implying that 2 neighbouring channels were correlated. This factor |
---|
| 888 | is now a user-selectable parameter, so that if you know how many |
---|
| 889 | spectral channels should be correlated, you can set the parameter |
---|
| 890 | FDRnumCorChan and the FDR calculation will be done correctly. |
---|
| 891 | |
---|
[542] | 892 | * Screen output now has more information on the growing threshold when |
---|
| 893 | the cube statistics are printed. |
---|
| 894 | |
---|
| 895 | |
---|
| 896 | Bug fixes: |
---|
| 897 | |
---|
[584] | 898 | * When reading in previous detections, there was a bug causing a |
---|
| 899 | segmentation fault. This has been fixed and made more robust. |
---|
| 900 | |
---|
[579] | 901 | * There was an apparent bug when writing out the reconstructed cubes |
---|
| 902 | to a FITS file that caused the new file to be very large. Changing |
---|
| 903 | the cfitsio function used has fixed this. |
---|
| 904 | |
---|
[574] | 905 | * Using NCP projections near the equator could result in a large |
---|
| 906 | stream of error messages, due to coordinate transformations being |
---|
| 907 | done in blank regions outside of the acceptable range of world |
---|
| 908 | coordinates. This has been fixed. |
---|
| 909 | |
---|
[542] | 910 | * The function that grows objects had a major bug, that stopped it |
---|
| 911 | working when flagAdjacent=false. This has been fixed and should work |
---|
| 912 | fine. |
---|
| 913 | |
---|
[616] | 914 | * The input parameter spectraTextFile was not being read |
---|
| 915 | properly. This has been remedied. |
---|
| 916 | |
---|
| 917 | * The units for the integrated flux were wrong for some types of pixel |
---|
| 918 | flux units. This has been fixed. |
---|
| 919 | |
---|
| 920 | * A minor bug caused incorrect calculation of the 20% widths. |
---|
| 921 | |
---|
[542] | 922 | * All calls to uint were changed to unsigned int, as some compilers |
---|
| 923 | had problems recognising that they were the same thing. |
---|
| 924 | |
---|
| 925 | * src/fitsHeader.cc was missing an include statement for stdlib.h, |
---|
| 926 | again causing some compilers to fail. |
---|
| 927 | |
---|
| 928 | |
---|
[529] | 929 | Duchamp version 1.1.7 (2009/01/16) |
---|
[520] | 930 | ---------------------------------- |
---|
| 931 | |
---|
| 932 | Improvements: |
---|
| 933 | |
---|
[522] | 934 | * The mask file that can be created with flagMask can now specify |
---|
| 935 | which object a given detected pixel belongs to, by taking the object |
---|
| 936 | ID as its value. This applies if you set flagMaskWithObjectNum=true |
---|
| 937 | (it defaults to false, which means each detected pixel has the value |
---|
| 938 | 1). Non-detected pixels still have the value 0. |
---|
[520] | 939 | |
---|
[535] | 940 | * The names of the output FITS files are now able to be specified |
---|
| 941 | directly by input parameters. These will override the default names |
---|
| 942 | that Duchamp provides. |
---|
| 943 | |
---|
[520] | 944 | * The Karma annotation file now specifies a font - previously it did |
---|
| 945 | not and so was at the mercy of whatever was specified in other |
---|
| 946 | annotation files being viewed at the same time. Please let me know |
---|
| 947 | if the font I've chosen (lucidasans-12) is not suitable. |
---|
| 948 | |
---|
| 949 | * The default flag, used in the absence of 'E', 'S' or 'N', is now '-' |
---|
| 950 | rather than blank. This will ensure that each column in the results |
---|
| 951 | file has something in it. |
---|
| 952 | |
---|
[522] | 953 | * The configure script is somewhat more robust to non-standard |
---|
| 954 | systems, particularly when the X11 libraries are in unusual |
---|
| 955 | places. It can also deal with the slightly different way that |
---|
| 956 | wcslib-4.3 installs itself. |
---|
| 957 | |
---|
[520] | 958 | * The installation part of the Makefile was altered so that the |
---|
| 959 | symbolic link Duchamp that points to Duchamp-1.1.7 does not have the |
---|
| 960 | absolute path encoded in it. This will enable the files to be moved |
---|
| 961 | around at a later date. |
---|
| 962 | |
---|
| 963 | Bug Fixes: |
---|
| 964 | |
---|
| 965 | * Fixed a bug that caused problems when the flux units were less than |
---|
| 966 | 5 characters long (e.g. 'K') |
---|
| 967 | |
---|
| 968 | * The new velocity width values were not getting proper headers in the |
---|
| 969 | VOTable output. This has been remedied. |
---|
| 970 | |
---|
| 971 | * Minor improvements to help non-pgplot use |
---|
| 972 | |
---|
| 973 | * Minor fix in WCS functionality. |
---|
| 974 | |
---|
| 975 | * Minor fixes to the FitsHeader class. |
---|
| 976 | |
---|
| 977 | * Improved FITS data reading, that doesn't require a nullarray |
---|
| 978 | array. This will reduce memory usage. |
---|
| 979 | |
---|
| 980 | * Improved subsection parsing, particularly for non-standard WCS |
---|
| 981 | systems. |
---|
| 982 | |
---|
| 983 | * Improving the memory allocation of the Cube class. |
---|
| 984 | |
---|
| 985 | * Fixed a bug that meant the growthThreshold values were sometimes |
---|
| 986 | being lost. |
---|
| 987 | |
---|
| 988 | * Improving the way the growing and merging is done, particularly in |
---|
| 989 | the case of non-adjacent merging. |
---|
| 990 | |
---|
[529] | 991 | * Fixed a scaling bug in the GaussSmooth function. |
---|
| 992 | |
---|
[520] | 993 | Other: |
---|
| 994 | |
---|
| 995 | * Numerous changes to the code that do not affect how Duchamp itself |
---|
| 996 | runs, but were necessary for code development with the Duchamp |
---|
| 997 | libraries (primarily as a part of the ASKAP code development). |
---|
| 998 | |
---|
[522] | 999 | |
---|
[482] | 1000 | Duchamp version 1.1.6 (2008/09/08) |
---|
[480] | 1001 | ---------------------------------- |
---|
| 1002 | |
---|
| 1003 | New features: |
---|
| 1004 | |
---|
| 1005 | * The velocity widths can now be quoted in two additional ways: the |
---|
| 1006 | full width at 50% of the peak flux (ie. the FWHM) and the full width |
---|
| 1007 | at 20% of the peak flux (w_50 and w_20 respectively). The w_50 |
---|
| 1008 | parameter is now quoted in the results printed to the screen |
---|
| 1009 | (instead of w_VEL), but all three are written to the results file. |
---|
| 1010 | |
---|
| 1011 | * The facility now exists to bypass the searching step and go straight |
---|
| 1012 | to the output stage using a list of previously detected objects. The |
---|
| 1013 | list is extracted from a previously-created log file. The user can |
---|
| 1014 | change the way the spectra are plotted (e.g. choose to plot |
---|
| 1015 | integrated rather than peak spectra), and select a subset of the |
---|
| 1016 | detected objects to be printed to individual postscript files. Use |
---|
| 1017 | the input parameter usePrevious (set to true) to use this facility, |
---|
| 1018 | and provide a list of objects using the objectList parameter |
---|
| 1019 | (eg. 1,2,4,7-10,15) |
---|
| 1020 | |
---|
[482] | 1021 | * A new parameter "growthThreshold" has been created, that goes with |
---|
| 1022 | "threshold". If you manually specify a threshold, and you wish to |
---|
| 1023 | grow detections, you need to manually specify a growthThreshold (in |
---|
| 1024 | flux units). |
---|
| 1025 | |
---|
[480] | 1026 | Bug fixes: |
---|
| 1027 | |
---|
[482] | 1028 | * Cubes that do not have a spectral axis (such as Stokes cubes) were |
---|
| 1029 | causing memory leaks and crashing, due to some assumptions of the |
---|
| 1030 | existence of the spectral axis. These bugs have been fixed, so that |
---|
| 1031 | Duchamp will run on such cubes, although the WCS transforms may not |
---|
| 1032 | always work appropriately. Please let me know via bug reports of |
---|
| 1033 | difficulties you encounter! |
---|
[480] | 1034 | |
---|
[482] | 1035 | * The growing function has had a few bugs fixed and is now more |
---|
| 1036 | efficient. |
---|
| 1037 | |
---|
| 1038 | * The FDR method was previously overriding any manually-specified |
---|
| 1039 | threshold. This has been fixed so that if the user specifies |
---|
| 1040 | threshold=X, then the FDR method is not called. |
---|
| 1041 | |
---|
| 1042 | * Some undefined things were happening with textual output when no |
---|
| 1043 | objects were detected. This has been fixed. |
---|
| 1044 | |
---|
| 1045 | * Memory leaks caused by FITS WCS irregularities have been fixed |
---|
| 1046 | (specifically, if a FITS header had NAXIS=2 but more than two WCS |
---|
| 1047 | axes were defined). |
---|
| 1048 | |
---|
| 1049 | |
---|
| 1050 | |
---|
[438] | 1051 | Duchamp version 1.1.5 (2008/03/20) |
---|
| 1052 | ---------------------------------- |
---|
| 1053 | |
---|
| 1054 | Bug fixes: |
---|
| 1055 | * A major bug was discovered in the calculation of integrated |
---|
| 1056 | fluxes. The flux was incorrectly being weighted by the spatial size |
---|
| 1057 | of the detection, resulting in a (often considerable) overestimation |
---|
[447] | 1058 | of the integrated flux. This has been corrected. |
---|
[438] | 1059 | |
---|
[447] | 1060 | * The beam size calculation was also incorrect, being out by a factor |
---|
| 1061 | of 1/ln(2). |
---|
[438] | 1062 | |
---|
[447] | 1063 | * The "make install" command previously failed to work properly if the |
---|
| 1064 | library had not been created. This has been fixed so that the |
---|
| 1065 | installation works even if there is no library file. |
---|
| 1066 | |
---|
| 1067 | New Features: |
---|
| 1068 | * You can now provide a new flux unit string, so that the pixel fluxes |
---|
| 1069 | will be converted to these new fluxes before any calculations are |
---|
| 1070 | done. This is done with the newFluxUnits input parameter. The new |
---|
| 1071 | units should be directly convertible from the old ones (given by the |
---|
| 1072 | BUNIT header -- e.g. if BUNIT = Jy/beam, you can give newFluxUnits |
---|
| 1073 | as mJy/beam, but not mJy). |
---|
| 1074 | |
---|
| 1075 | * You can now specify the precision used in the output files for flux, |
---|
| 1076 | velocity and S/N ratio columns, via new input parameters precFlux, |
---|
| 1077 | precVel and precSNR. These will apply to the VOTable output as well |
---|
| 1078 | as the text table and information on the spectral plots. |
---|
| 1079 | |
---|
| 1080 | * The Karma annotation files previously provided just a circle at the |
---|
| 1081 | spatial location of the detected object. You now have the option to |
---|
| 1082 | draw a border around the detected pixels (in a similar manner to the |
---|
| 1083 | PGPLOT moment maps). Karma does not do this perfectly, so the lines |
---|
| 1084 | may not line up exactly with the pixel borders, so the option |
---|
| 1085 | remains to keep using the circles. This is controlled by the |
---|
| 1086 | parameter "annotationType", with possible options being "borders" |
---|
| 1087 | (the default) or "circles". |
---|
| 1088 | |
---|
| 1089 | * There is a new function getMetadata() that loads the header and WCS |
---|
| 1090 | data, but no pixel information. This is only of interest if you are |
---|
| 1091 | doing code development with the Duchamp library -- it does not |
---|
| 1092 | affect the running of Duchamp itself. |
---|
| 1093 | |
---|
[425] | 1094 | Duchamp version 1.1.4 (2008/02/15) |
---|
| 1095 | ---------------------------------- |
---|
| 1096 | |
---|
| 1097 | Most of the changes incorporated in this update result from ASKAP code |
---|
| 1098 | development (that makes use of some of the Duchamp functionality), |
---|
| 1099 | but do not actually affect the way Duchamp runs (other than, in a |
---|
| 1100 | couple of cases, making it a bit faster). Changes that are |
---|
| 1101 | relevant for regular users of Duchamp are as follows: |
---|
| 1102 | |
---|
| 1103 | * A new option has been made available (thanks to Mary Putman et al |
---|
| 1104 | for the suggestion!) to save the spectra of all detected objects in |
---|
| 1105 | a text file. This has the form of one column for the spectral |
---|
| 1106 | coordinates and one column of fluxes for each object. This is |
---|
| 1107 | enabled by the input parameters flagTextSpectra and spectraTextFile. |
---|
| 1108 | |
---|
| 1109 | * Slight changes to the output include he formatting of the way the |
---|
| 1110 | detected objects are written to the log file. This meant the |
---|
| 1111 | verification files were also updated. Also the cube statistics are |
---|
| 1112 | not printed to the results file if a user threshold is specified (as |
---|
| 1113 | they are not calculated!). |
---|
| 1114 | |
---|
| 1115 | * The determination of beam size has been made more reliable, as has |
---|
| 1116 | the BUNIT determination. |
---|
| 1117 | |
---|
| 1118 | * Fixed a bug that meant source merging was not done for 2D images |
---|
| 1119 | (not usually a problem, as the source-finding takes care of this, |
---|
| 1120 | but came up in parallelisation development). |
---|
| 1121 | |
---|
[406] | 1122 | Duchamp version 1.1.3 (2008/01/08) |
---|
| 1123 | ---------------------------------- |
---|
[404] | 1124 | |
---|
| 1125 | A minor update that just improves the build process. The location of |
---|
| 1126 | the wcslib include files was not specified correctly, so that some |
---|
| 1127 | machines were unable to find them. The configure script has been fixed |
---|
| 1128 | so that the compilation should work in all cases. |
---|
| 1129 | |
---|
[405] | 1130 | Some minor changes have also been made to the code in the PixelMap |
---|
[412] | 1131 | directory, and to param.cc, to fix warnings or errors that may appear |
---|
| 1132 | in compilation. |
---|
[404] | 1133 | |
---|
[405] | 1134 | However, there are no changes to the actual workings of the code in |
---|
| 1135 | this minor version, so if you have a working version of Duchamp 1.1.2 |
---|
| 1136 | there is probably no reason to update. |
---|
| 1137 | |
---|
[389] | 1138 | Duchamp version 1.1.2 (2007/12/07) |
---|
| 1139 | ---------------------------------- |
---|
[349] | 1140 | |
---|
[363] | 1141 | Compilation: |
---|
| 1142 | |
---|
[349] | 1143 | * The compilation had problems working correctly when the cfitsio and |
---|
[373] | 1144 | wcs libraries were not in standard locations. The configure script |
---|
[349] | 1145 | has been tweaked to make sure the libraries are found. |
---|
| 1146 | |
---|
| 1147 | * Problems with compiling in the absence of pgplot have been fixed, |
---|
| 1148 | and it should now compile fine. |
---|
| 1149 | |
---|
[362] | 1150 | * Improved the configure script for use with Mac OS X and gfortran. |
---|
[349] | 1151 | |
---|
[363] | 1152 | |
---|
| 1153 | Bugfixing: |
---|
| 1154 | |
---|
[362] | 1155 | * A major problem with the text-based output was fixed. The widths of |
---|
| 1156 | the columns were not being calculated correctly, and were running |
---|
[373] | 1157 | together. This should no longer be the case. |
---|
[349] | 1158 | |
---|
[374] | 1159 | * There was a bug in the way Duchamp interpreted spectral axes, |
---|
| 1160 | particularly AIPS types such as FELO-HEL, leading to incorrect |
---|
| 1161 | scaling of the velocity axis. This has been fixed, so that |
---|
| 1162 | non-standard types are now dealt with appropriately and the velocity |
---|
| 1163 | scaling should be accurate. |
---|
[362] | 1164 | |
---|
[376] | 1165 | * Another bug meant the beam correction was always applied to the |
---|
| 1166 | integrated spectra, regardless of whether the flux units involved |
---|
| 1167 | the beam (e.g. Jy/beam). This has been fixed. Note that the values |
---|
| 1168 | of the integrated flux presented in the results table were always |
---|
| 1169 | calculated correctly. |
---|
| 1170 | |
---|
[389] | 1171 | * Other minor changes to improve the speed and efficiency, especially |
---|
| 1172 | of the merging code. |
---|
| 1173 | |
---|
[363] | 1174 | New user parameters: |
---|
| 1175 | |
---|
[381] | 1176 | * There is now the possibility to save a FITS file that contains a |
---|
| 1177 | mask array, indicating where the detected objects are. This is |
---|
| 1178 | governed by the flagOutputMask parameter. |
---|
| 1179 | |
---|
[363] | 1180 | * The header information that is printed at the start of the results |
---|
| 1181 | file -- that is, the list of parameters, the statistics of the cube, |
---|
| 1182 | and the number of detections -- can now be written to a separate |
---|
| 1183 | file. Set the flagSeparateHeader parameter to true or 1 and it will |
---|
| 1184 | go to the file indicated by the headerFile parameter (the default is |
---|
| 1185 | duchamp-Results.hdr). |
---|
| 1186 | |
---|
[362] | 1187 | * A "scaleMax" parameter has been added, so that the wavelet |
---|
| 1188 | reconstruction can include only a specified range of scales (for |
---|
[373] | 1189 | instance, if one wants to search just for narrow features such as |
---|
[362] | 1190 | absorption lines). |
---|
| 1191 | |
---|
[389] | 1192 | * A "flagRobustStats" parameter has been added. This allows the user |
---|
| 1193 | to elect to use robust statistics (median and median absolute |
---|
| 1194 | deviation from the median) to estimate the noise parameters. If set |
---|
| 1195 | to false, the mean and standard deviation will be used. The default |
---|
| 1196 | value is true. |
---|
[362] | 1197 | |
---|
[369] | 1198 | New Feature: |
---|
[362] | 1199 | |
---|
[369] | 1200 | * When Duchamp is run on a 2D image (i.e. with no spectral output), it |
---|
| 1201 | now produces a postscript file that shows information each |
---|
| 1202 | individual source plus the image cutout of the source. This is |
---|
| 1203 | similar to the spectral output file, but without the spectra. The |
---|
| 1204 | filename is given by the spectraFile parameter. |
---|
| 1205 | |
---|
[381] | 1206 | * Ability to save a FITS file containing a mask array, with pixel |
---|
| 1207 | values of 1 for pixels in a detected object, and 0 elsewhere. |
---|
[369] | 1208 | |
---|
[381] | 1209 | |
---|
[328] | 1210 | Duchamp version 1.1.1 (2007/07/20) |
---|
| 1211 | ------------------------------------ |
---|
| 1212 | |
---|
[329] | 1213 | Minor update to the release, with just a few changes: |
---|
[328] | 1214 | |
---|
| 1215 | * The verification script was generating diffs due to differences in |
---|
| 1216 | the precision of some calculations when done on different machines. |
---|
| 1217 | One of these was the integrated flux, and this has been corrected so |
---|
| 1218 | that the same value should appear on all machines. |
---|
| 1219 | The verification script has also changed so that just the number of |
---|
| 1220 | sources and their positions are tested, as well as the |
---|
| 1221 | logfiles. This should avoid the reporting of spurious differences. |
---|
| 1222 | |
---|
| 1223 | * The grey-scale used in the image cutouts (in the spectral plots) has |
---|
| 1224 | been inverted. This makes it consistent with the scale used in the |
---|
| 1225 | maps, and hopefully easier to see when printing. |
---|
| 1226 | |
---|
[338] | 1227 | * The configure/make system has been altered to make it easier to |
---|
| 1228 | install, and to specify different external libraries. In particular, |
---|
| 1229 | it is now not necessary to have PGPLOT installed on your system to |
---|
| 1230 | run Duchamp. In the absence of PGPLOT, Duchamp will run as normal, |
---|
| 1231 | just without any graphical output. Some source code needed to be |
---|
[344] | 1232 | restructured to make this work. Please read the README file, or the |
---|
| 1233 | Installation appendix in the User's Guide, for complete details. |
---|
[328] | 1234 | |
---|
[329] | 1235 | * The time of completion is now written to the log file, so that the |
---|
| 1236 | user can have some idea of how long the program took. |
---|
[328] | 1237 | |
---|
| 1238 | |
---|
[310] | 1239 | Duchamp version 1.1 (2007/05/17) |
---|
[259] | 1240 | ------------------------------------ |
---|
| 1241 | |
---|
| 1242 | Changes made since the last numbered release: |
---|
| 1243 | |
---|
[295] | 1244 | EFFICIENCY OF EXECUTION: |
---|
| 1245 | |
---|
[259] | 1246 | * Major change to the way detections are stored. They are now recorded |
---|
| 1247 | via run-length encoding in the x-y plane, and stored as collections |
---|
| 1248 | of channel-maps. This improves the memory usage and the speed of |
---|
[298] | 1249 | execution (particularly for routines such as the merging |
---|
| 1250 | routines). The memory usage has also been improved by changing the |
---|
| 1251 | way the list of detected objects is stored. |
---|
[259] | 1252 | |
---|
[295] | 1253 | SMOOTHING: |
---|
| 1254 | |
---|
[279] | 1255 | * Addition of ability to spatially smooth the cube before |
---|
| 1256 | searching. This is done with a Gaussian kernel, the size and shape |
---|
[287] | 1257 | of which can be specified by the user, using the parameters kernMaj |
---|
| 1258 | & kernMin (which are the FWHM for the major & minor axes -- if |
---|
| 1259 | kernMin is not given it is assumed to match kernMaj) and kernPA (the |
---|
| 1260 | position angle of the major axis). There is a new parameter |
---|
[279] | 1261 | smoothType that distinguishes this method from the spectral (Hanning) |
---|
| 1262 | smoothing already in use. |
---|
| 1263 | |
---|
[295] | 1264 | DETECTIONS: |
---|
| 1265 | |
---|
[264] | 1266 | * Changed the way detection is done -- now only search in 2D images, |
---|
| 1267 | keeping all detections (ie. no minimum-pixel requirement). This |
---|
| 1268 | should be the same as doing both the 1D and 2D searches with the |
---|
| 1269 | minimum pixel requirement in, but simpler. The rejection is done at |
---|
[295] | 1270 | the end after all the merging and growing has been done. This leads |
---|
| 1271 | to a larger number of intermediate detections (ie. the number |
---|
| 1272 | before merging), which may increase the run-time slightly, although |
---|
| 1273 | this is offset by the changes to the efficiency (see above). |
---|
[264] | 1274 | |
---|
| 1275 | * Increased the range over which objects can be grown to match the |
---|
| 1276 | threshSpatial & threshVelocity parameters, as well as rejecting new |
---|
| 1277 | pixels based on the BLANK and MW tests. |
---|
| 1278 | |
---|
[295] | 1279 | INPUTS: |
---|
[259] | 1280 | |
---|
[287] | 1281 | * There has been a subtle change in the way BLANK pixels are dealt |
---|
| 1282 | with. To enable trimming of BLANK pixels, users should use the new |
---|
| 1283 | parameter flagTrim. The parameters flagBlankPix and blankPixVal are |
---|
[295] | 1284 | no longer accessible via the parameter file -- warning messages are |
---|
| 1285 | given if they are provided in the parameter file. |
---|
[287] | 1286 | |
---|
[295] | 1287 | * Added ability to specify a statsec, so that the statistics are only |
---|
| 1288 | calculated from a given subsection of the cube, rather than the full |
---|
| 1289 | cube. |
---|
| 1290 | |
---|
| 1291 | * The subsections can also specify the ability to remove a border of n |
---|
| 1292 | pixels from the edges of an axis (ie. n from the start and from the |
---|
| 1293 | end) -- as requested in Trac ticket #5. |
---|
| 1294 | |
---|
| 1295 | * Changed the default value of the reconDim parameter from 3 to 1, and |
---|
| 1296 | the default value of the flagATrous parameter to false. |
---|
| 1297 | |
---|
| 1298 | OUTPUTS: |
---|
| 1299 | |
---|
[279] | 1300 | * The output now includes three different estimates of the "centre" of |
---|
| 1301 | the detection: peak location, centroid (flux-weighted), or average. |
---|
| 1302 | |
---|
[295] | 1303 | * Some slight improvements to the user feedback during execution. |
---|
| 1304 | |
---|
[282] | 1305 | * Spectral output now includes the baseline, if one was fitted. The |
---|
| 1306 | format of the plot headers is slightly changed, to stop information |
---|
| 1307 | falling off the edge of the page. |
---|
[279] | 1308 | |
---|
[295] | 1309 | * Added command-line option -x to directly disable the PGPLOT X-window |
---|
| 1310 | map plotting. This overrides the setting of flagXOutput in the |
---|
| 1311 | parameter file. |
---|
[259] | 1312 | |
---|
[295] | 1313 | * Fallback spectral units (in case the FITS header fails to record |
---|
| 1314 | them) changed to SPC, but code has been fixed so that any problem |
---|
| 1315 | should be caught before this becomes an issue. |
---|
| 1316 | |
---|
| 1317 | BUGFIXES: |
---|
| 1318 | |
---|
[259] | 1319 | * Fixed bug (Trac ticket #4) that meant the velocity units were not |
---|
| 1320 | correctly dealt with. Duchamp should be more robust for different |
---|
| 1321 | velocity axis setups now. |
---|
| 1322 | |
---|
| 1323 | * Fixed bug (ticket #9) with the VOTable output, where the tags were |
---|
| 1324 | not closing. |
---|
| 1325 | |
---|
[305] | 1326 | * Fixed a bug that meant the integrated fluxes were not calculated |
---|
| 1327 | properly -- no allowance was made for the number of spatial |
---|
| 1328 | pixels. This should also work properly for 2D images now as well. |
---|
| 1329 | |
---|
[264] | 1330 | * Fixed minor bug in calculating the flux threshold from the p-value |
---|
| 1331 | threshold when the FDR method is used. This did not affect the |
---|
| 1332 | actual thresholding, merely the quoted flux threshold in the results |
---|
| 1333 | file. Also, the MW channels are kept out of the p-value threshold |
---|
| 1334 | determination if they are being flagged. |
---|
| 1335 | |
---|
[259] | 1336 | |
---|
| 1337 | |
---|
[211] | 1338 | Duchamp version 1.0.7 (2006/11/22) |
---|
| 1339 | ---------------------------------- |
---|
| 1340 | |
---|
| 1341 | One new feature, and some improvements and bug-fixes. |
---|
| 1342 | |
---|
[264] | 1343 | * The user can now elect to Hanning-smooth the spectral direction of |
---|
| 1344 | the cube before the searching is done. This can be done instead of the |
---|
| 1345 | wavelet reconstruction (although if both are selected, the |
---|
| 1346 | reconstruction takes precendence). This functionality is switched on |
---|
| 1347 | and off by the flagSmooth parameter, and the width of the Hanning |
---|
| 1348 | kernel is governed by the hanningWidth parameter. |
---|
[211] | 1349 | |
---|
[264] | 1350 | * The smoothed array can also be written to a FITS file and read in at |
---|
| 1351 | the start in the same manner as the reconstructed array. |
---|
[211] | 1352 | |
---|
[264] | 1353 | * Several improvements have been made to the memory |
---|
| 1354 | management. Several memory leaks were fixed, and the memory usage of |
---|
| 1355 | Duchamp is considerably less, which will be a help for running it on |
---|
| 1356 | large cubes. The speed of some routines has also been improved, by |
---|
| 1357 | removing unnecessarily repetitive loops. |
---|
[211] | 1358 | |
---|
[287] | 1359 | * The sorting routines have been changed, and should now be slightly quicker |
---|
[215] | 1360 | (and a bit more robust). |
---|
| 1361 | |
---|
[287] | 1362 | * Enabled the scale bar (plotted on the 0th moment map in the spectral |
---|
| 1363 | output file) to be able to deal with much finer spatial scales (as |
---|
| 1364 | may be expected from VLBI data). |
---|
[211] | 1365 | |
---|
[215] | 1366 | * Other minor changes to code and presentation. |
---|
[211] | 1367 | |
---|
| 1368 | |
---|
[194] | 1369 | Duchamp version 1.0.6 (2006/11/01) |
---|
| 1370 | ---------------------------------- |
---|
| 1371 | |
---|
| 1372 | Some incremental improvements and changes to the code: |
---|
| 1373 | |
---|
| 1374 | * The statistics used for the detection are now calculated once for |
---|
| 1375 | the entire cube, rather than being calculated separately for each |
---|
| 1376 | channel map and spectrum. This results in a uniform threshold value |
---|
| 1377 | across the entire cube. The way the statistics calculations are |
---|
| 1378 | implemented in the code was changed, using a new statistics class. |
---|
| 1379 | |
---|
| 1380 | * This means we can report a peak signal-to-noise value for each |
---|
| 1381 | detection. This is given in the text-based output, as well as in the |
---|
| 1382 | summary information above the spectral output for each source. |
---|
| 1383 | |
---|
[195] | 1384 | * The user can now elect not to have the moment map displayed in a |
---|
| 1385 | PGPlot window, through the use of the new flagXOutput |
---|
| 1386 | parameter. This should help in cases of running Duchamp on a dumb |
---|
| 1387 | terminal (with no X-display capabilities), or as part of a batch |
---|
| 1388 | script where the continual popping-up of the PGPlot window might |
---|
| 1389 | become annoying. |
---|
| 1390 | |
---|
[265] | 1391 | * There are different Flags reported for the case of an object lying on |
---|
[194] | 1392 | the spatial edge and spectral edge of the cube (E and S respectively). |
---|
| 1393 | |
---|
| 1394 | * A few minor bug fixes: |
---|
| 1395 | - When providing a subsection, any axes with the range given by * |
---|
| 1396 | had the pixel values offset incorrectly. This has been fixed. |
---|
| 1397 | - Negative searches now correctly invert the reconstructed array |
---|
| 1398 | when it is read in from a file. |
---|
| 1399 | |
---|
| 1400 | * Other minor changes to the code, to improve memory handling and |
---|
| 1401 | remove redundant arrays and variables. |
---|
| 1402 | |
---|
| 1403 | |
---|
[146] | 1404 | Duchamp version 1.0.5 (2006/09/06) |
---|
[142] | 1405 | ---------------------------------- |
---|
| 1406 | |
---|
[146] | 1407 | Since version 1.0, there have been a range of mostly minor |
---|
| 1408 | changes. These are generally bug-fixes, thanks to feedback from a |
---|
[157] | 1409 | number of users, as well as a few extra features. |
---|
[146] | 1410 | |
---|
[157] | 1411 | Here is a summary of the changes since version 1.0: |
---|
[142] | 1412 | |
---|
[157] | 1413 | USER INTERFACE: |
---|
[146] | 1414 | |
---|
[142] | 1415 | * The user is now able to enter the value of flag parameters in the |
---|
| 1416 | parameter file as strings, as well as integers (so one can enter |
---|
| 1417 | true or 1 to give the same result). |
---|
| 1418 | |
---|
[157] | 1419 | GRAPHICAL OUTPUT: |
---|
| 1420 | |
---|
[142] | 1421 | * Added a new function that draws the edge of the blank region on the |
---|
[146] | 1422 | maps and image cutouts. There is a new flag parameter -- |
---|
| 1423 | drawBlankEdges -- that controls the use of this function (the |
---|
| 1424 | default is true). |
---|
| 1425 | Also, the edge of the field is plotted on the image cutouts as a |
---|
| 1426 | yellow line. This distinguishes it from the purple blank pixel |
---|
| 1427 | dividing line. |
---|
[142] | 1428 | |
---|
[146] | 1429 | * The size of the tick mark in the image cutout (indicating the |
---|
| 1430 | spatial scale of the image) is now adaptable, so that it shows the |
---|
| 1431 | scale that best fits the image (ranging from 1 arcsec to 15 |
---|
| 1432 | degrees). (This is a change from the previous standard length of 15 |
---|
| 1433 | arcmin.) |
---|
[142] | 1434 | |
---|
[113] | 1435 | * The zoomed spectrum had its flux scale determined by all points in |
---|
[146] | 1436 | the zoom box,including those flagged by the Milky Way (MW) |
---|
| 1437 | range. This has been fixed so that any MW channels will not affect |
---|
| 1438 | the flux scaling, potentially improving the appearance of objects |
---|
| 1439 | detected close in velocity to strong MW emission or absorption. |
---|
[112] | 1440 | |
---|
[157] | 1441 | * Improved Karma Annotation file output, so that files without good |
---|
| 1442 | WCS are dealt with appropriately. |
---|
| 1443 | |
---|
| 1444 | TEXT-BASED OUTPUT: |
---|
| 1445 | |
---|
[113] | 1446 | * The position resolution in the IAU-format names has been increased, |
---|
| 1447 | so that distinct objects close to one another are more readily |
---|
| 1448 | distinguished. Overlapping sources at different velocities may |
---|
| 1449 | still have the same name, but this is a more general problem. |
---|
[112] | 1450 | |
---|
[146] | 1451 | * The presentation of the results in tabular format has been improved, |
---|
| 1452 | so that the precision of faint sources is sufficient to show their |
---|
| 1453 | flux, for instance, is not 0. This also applies to the information |
---|
| 1454 | presented above the spectral plots. |
---|
[112] | 1455 | |
---|
[146] | 1456 | * Improved error and warning reporting, so that the formatting and |
---|
| 1457 | presentation of information is clearer. |
---|
| 1458 | |
---|
[157] | 1459 | FITS I/O RELATED: |
---|
| 1460 | |
---|
[172] | 1461 | * The previous version was did not deal well with 4 (or greater) |
---|
| 1462 | dimensions in the FITS file -- the memory allocation was badly done, |
---|
| 1463 | and the axes needed to be in a particular order. This has been |
---|
| 1464 | fixed, so that the FITS I/O routines can now handle any sized FITS |
---|
| 1465 | file, with axes in any order (as long as there are two spatial and one |
---|
| 1466 | spectral axes). |
---|
[157] | 1467 | |
---|
| 1468 | * When the FITS file does not have a rest frequency defined, there is |
---|
| 1469 | no way to transform the frequency axis into velocity. In this case, |
---|
| 1470 | the spectral axis is left as frequency, and put into units of MHz. |
---|
| 1471 | |
---|
[172] | 1472 | * If the beam size is not indicated by the FITS header (through the |
---|
| 1473 | BMAJ and BMIN keywords), the user can manually specify the size |
---|
| 1474 | through the parameter file (using parameter beamSize). |
---|
| 1475 | |
---|
| 1476 | * The FITS I/O routines make use of the command fits_file_exists. This |
---|
| 1477 | was introduced into the CFITSIO package from version 2.5, so Duchamp |
---|
| 1478 | will only work with this version or higher. Version 3+ is preferred. |
---|
| 1479 | |
---|
[157] | 1480 | OTHER BUG-FIXING: |
---|
| 1481 | |
---|
| 1482 | * Several bugs related to the blank-pixels were dealt with. |
---|
| 1483 | The correct values were not propagating through correctly, meaning |
---|
| 1484 | that the default values were being used. Also, there was the |
---|
| 1485 | potential for blank pixels to be detected when the FDR method was |
---|
| 1486 | used. Finally, the image cutout displays occasionally did not |
---|
| 1487 | obscure the blank pixels. All these problems should be fixed now. |
---|
| 1488 | |
---|
| 1489 | * The FDR setup routine was occasionally failing with a segmentation |
---|
| 1490 | fault, due to it accessing unallocated memory. This has been fixed. |
---|
| 1491 | |
---|
| 1492 | * Fixed bugs that affected the way 2D images (rather than 3D cubes) |
---|
| 1493 | were dealt with. The minChannels test failed when minChannels=0. |
---|
| 1494 | |
---|
[165] | 1495 | * If there is no beam information in the FITS header, the user can now |
---|
| 1496 | enter a beam size as a parameter. |
---|
| 1497 | |
---|
[146] | 1498 | * Other minor fixes to the code, to improve its structure and |
---|
| 1499 | robustness. |
---|
| 1500 | |
---|
| 1501 | |
---|
[112] | 1502 | Duchamp version 1.0 (2006/06/30) |
---|
| 1503 | -------------------------------- |
---|
| 1504 | |
---|
[113] | 1505 | The first full release version. |
---|
| 1506 | |
---|
| 1507 | Several major changes compared to previous version: |
---|
| 1508 | |
---|
| 1509 | * Incorporated a FitsHeader class, to keep track of header information |
---|
| 1510 | (including WCS) from the FITS file. All units-related calculations |
---|
| 1511 | are done with this class, such as conversion to velocity, and |
---|
| 1512 | pixel-to-WCS conversion. The main advantage of this is improved |
---|
| 1513 | speed of execution, more adaptable to different units, and improved |
---|
| 1514 | code (easier for me!). |
---|
| 1515 | |
---|
| 1516 | * Able to select the dimensionality of the reconstruction, rather than |
---|
| 1517 | just doing it in 3-D. |
---|
| 1518 | |
---|
| 1519 | * Robust text output, so that the columns are sized correctly given |
---|
| 1520 | the data being written, and the relevant units (derived from the |
---|
| 1521 | FITS header) are included in the output table. |
---|
| 1522 | |
---|
| 1523 | * Improved the way the reconstructed image is saved and read back in, |
---|
| 1524 | with a better naming scheme and a better set of new FITS header |
---|
| 1525 | keywords. The MW headers are now not written. |
---|
| 1526 | |
---|
| 1527 | Other, more minor changes include: |
---|
| 1528 | |
---|
| 1529 | * MW channels now not set to 0, but just ignored for searching |
---|
| 1530 | purposes (and for the scaling of the spectral output -- they are |
---|
| 1531 | plotted though and highlighted with a hashed box). |
---|
| 1532 | |
---|
| 1533 | * The scale bar in the moment map in the spectral output file has its |
---|
| 1534 | length indicated. |
---|
| 1535 | |
---|
| 1536 | * Improved VOTable output, with more information about the way Duchamp |
---|
| 1537 | was run. |
---|
| 1538 | |
---|
| 1539 | * Made sure all statistics calculations in the reconstruction are |
---|
| 1540 | based on robust (ie. median) methods. |
---|
| 1541 | |
---|
| 1542 | Also moved to an autoconf based configure/make compilation, for ease of use. |
---|
| 1543 | |
---|
| 1544 | |
---|
| 1545 | Duchamp version 0.9.2 (2006/06/27) |
---|
| 1546 | -------------------------------- |
---|
| 1547 | |
---|
| 1548 | * Added the use of warning flags for detections: for either edge |
---|
| 1549 | location or negative enclosed flux. |
---|
| 1550 | |
---|
| 1551 | * A new command line option added so that the user can specify a FITS |
---|
| 1552 | file to be searched with the default parameters, rather than giving |
---|
| 1553 | a full parameter file. |
---|
| 1554 | |
---|
| 1555 | * The scale bar on the moment cutout now works in general case, using |
---|
| 1556 | an iterative process to get to the correct length. |
---|
| 1557 | |
---|
| 1558 | * RA axes are now done correctly on the full-scale maps. |
---|
| 1559 | |
---|
| 1560 | * Various coding fixes, improving the readability of the code, |
---|
| 1561 | particularly regarding the declaration of temporary variables. |
---|
| 1562 | |
---|
| 1563 | * Changed the way the time of execution is called : now using time.h |
---|
| 1564 | functions, rather than a system call. |
---|
| 1565 | |
---|
| 1566 | * Changed output in Detection/outputDetection.cc for the pixel |
---|
| 1567 | information of detected objects (the info printed above the spectral |
---|
| 1568 | plots) -- now print out number of voxels in object, and have |
---|
| 1569 | improved the formatting a little. |
---|
| 1570 | |
---|
| 1571 | * Improved the functionality of saving the FITS file containing the |
---|
| 1572 | reconstructed array. Added ability to save and read back in the MW |
---|
| 1573 | parameters when saving a reconstructed cube (if a reconstructed cube |
---|
| 1574 | has different MW range to that being considered, it would cause |
---|
| 1575 | problems). ReadRecon now just returns a FAILURE and will reconstruct |
---|
| 1576 | the cube anew. |
---|
| 1577 | |
---|
| 1578 | * Changed default value of flagGrowth to 0. |
---|
| 1579 | |
---|
| 1580 | |
---|
| 1581 | |
---|
| 1582 | Duchamp version 0.9 (2006/05/05) |
---|
| 1583 | -------------------------------- |
---|
| 1584 | |
---|
| 1585 | First public release version. |
---|